David Penny

Edward David Penny CNZM FRSNZ (born 1939 in Taumarunui) is a theoretical and evolutionary biologist from New Zealand.

He has researched the nature of evolutionary transformations, and is widely published in the fields of phylogenetic tree, genetics and evolutionary biology.

Penny's contributions to science have been recognised with several awards and honours, and acceptance into the National Academy of Sciences.

Penny attended New Plymouth Boys' High School before gaining undergraduate degrees in botany and chemistry at the University of Canterbury.

He completed his PhD in botany at Yale University in 1965 and later worked as a postdoctoral researcher at McMaster University.

He returned to New Zealand in 1966 and joined the staff at Massey University, within the Department of Plant Biology, School of Biological Sciences, Institute for Molecular BioSciences, and Institute of Fundamental Sciences and in 2005 Penny was named a Distinguished Professor.

It has been said that the paper Construction of Phylogentic Trees (1967) was what first made Penny interested in tracing the process of evolution.

In the 1970s Penny looked into how genetic information on all forms of life could be used to investigate questions such as the origin of life, the occurrence of evolution and the relationship between species and communities.

He helped to develop "mathematical techniques and computer programmes to analyse DNA sequences and construct evolutionary trees...[developing]... new insights that support the idea that humans evolved in and then migrated from Africa and that the first forms of life were based on the simpler RNA molecule rather than DNA".

They claimed the writers had "delivered biased opinions" that presented "an introns-early (and eukaryotes-first) view of early evolution that was current in 1980 and that was shown by conventional scientific criteria to be untenable over a decade ago".

In the same journal, Penny et al. responded that new information from cellular and molecular genomics provided previously unavailable information on eukaryote origins.

They agreed it was "still premature to decide between introns first, early, or late...nevertheless, our primary conclusion is that there is good progress on understanding the complexity of the ancestral eukaryote cell".

Penny was also part of a research team that explored theories for eukaryote origins and noted some of these ignore life history and ecological principles, and it was necessary to challenge predictions there was a long period in early life with no predators.

The authors concluded that their results were "consistent with the expectation that the ability to gain energy via engulfment of other unicells evolved early during evolution...thus from first principles, it is unlikely that there ever was an extended period (1–3 billion years) when there were no predators that lived by engulfing smaller cells".

This had implications when considering the most likely time that eukaryotes emerged, and challenged the view that these cells arose sometime between 9.85 ~ 2.75 billion years ago.

From the starting point that phagocytotic predators were almost exclusively eukaryotic, the paper maintained that these existed earlier in evolution.

In looking to clarify a sound basis of classification, in 1982 he entered the controversy about whether relationships between organisms should be expressed in "evolutionary terms, or on clusters based on overall similarity", and concluded that retaining the original data supported sound classification.

Penny was involved in research teams that explored tree building methods.

In 1985, he collaborated on work that evaluated the reliability of these, and the research paper concluded that there needed to be a balance between the traditional approach of "weighting the characters" and a computer-based approach utilizing the growing awareness of numerical taxonomy.

One of the authors of that paper, Walter Fitch, reflected in 1988 that the inspiration for their 1967 research was to develop a computer programme that would break the genetic code and develop a "molecular paleontological record in proteins and nucleic acid".

Penny's early research challenged the theories of evolution at the time.

Another paper in 1992, while noting at times the conventional methods were reliable, also presented a new approach.

This was known as LogDet and according to the authors of the paper, "[allowed] tree-selection methods to consistently recover the correct tree when sequences evolve under simple asymmetric models...produce sequences of different nucleotide compositions...and are more realistic than most standard models".

In 1993 he co-authored a research paper that took the position progress was being made with methods for evolutionary trees.

In the Abstract, the authors explaind the signals of macromolecules from a common history and clarified the intention of the research as being to discuss methods that were "efficient (fast), consistent, powerful, robust, and falsifiable", for inferring evolutionary trees from these patterns or signals.

The paper concludeed that most methods of tree inference needed corrections, but "the recognition that methods may be both efficient and consistent [was] also useful".

In 1998 he co-authored a paper providing compelling DNA-based evidence that the Māori migration to New Zealand included between 50 and 100 females, a finding noted by the authors as "entirely consistent with Māori oral history as well as the results of recent canoe voyages recreating early trans-oceanic voyages".

From 2002 to 2010 Penny co-led the Allan Wilson Centre, one of the original New Zealand Centres of Research Excellence hosted at Massey University.

A paper co-authored by Penny in 2006, challenged the prevailing view at the time that eukaryotes had evolved by genome fusion between archaea and bacteria, suggesting they "were more likely to have been reduced by sequence loss and cellular simplification after the possible emergence of a predatory eukaryote. This research was significant because it suggested that modern eukaryote and prokaryote cells had long followed separate evolutionary trajectories, confirming "that evolution does not proceed monotonically from the simpler to the more complex". Penny told NBC News the results may been surprising to some, but stressed that there was little evidence of the fusion theory explaining "the special genetic and cellular features of the eukaryotes". He suggested it was an example of evolution being "backwards, sideways and occasionally forward". A group of international scientists disputed the findings in the 2006 paper.

After working as a member of a team researching bird evolution in 2008, Penny co-authored the paper of the work which confirmed there were problems in this area for evolutionary biologists.

The writers said it was partly due to scientists being mislead by "convergence of morphology...[and]...problems and phylogenies based on short DNA sequences".

The paper further attempted to resolve issues around "the relationships between clades and the timing of the evolution of birds", and based on the phylogenetic data, concluded that "seven Metave species do not share a common evolutionary history within the Neoaves".

Resolution of controversies around the understanding of the evolutionary relationship between modern birds due to this polytomy at the base of the Neonaves, is the focus of later research in which Penny participated.

New developments suggested in this paper included reducing noise level and more accurate use of formulae to find predefined groupings in the optimal tree.

Significantly, the research reported the existence of nine new mitochondrial genomes [which] "support a major diversification of at least 12 neoavian lineages in the Late Cretaceous".

Penny has also been involved in 2010 research that suggested some ratites nested and therefore had previously flown.

One example, the extinct moa, closely related to the tinamou breed of birds from South America, according to Penny may have flown or "was blown, to New Zealand via Antarctica before it froze over".

Until it closed in 2015, the centre had a focus on researching the evolution and ecology of New Zealand and Pacific plant and animal life.

After retiring in 2017 he became a Professor Emeritus.

His research has focused on theoretical biology, molecular evolution, human evolution, and the history of science.